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Starter - How to create a correct .psf file (carbon)
#38294 06/29/21 02:12 PM
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Hello,

I am a recent starter regarding the CHARMM forcefield. I am trying to learn it the best I can, however my field of interest is carbonaceous materials (graphene / carbon nanotubes / fullerenes) and despite the number of tutorials I have watched or read, I am still encountering problems for generating the required .psf file.

Basically, I have created a model of a fluoride-functionalized fullerene in Avogadro 1.2, and exported the .pdb file. I am providing it as an attachment here.

All I need at the moment is to obtain an accurate .psf file. From what I have read on this forum and other sources, I understand that most of the time fullerenes are parameterized as the sp2 aromatic carbon. I have also read articles that provide some experimental values regarding C-C interactions specific to carbon nanotubes. From what I have read, manually building or changing existing .psf files is not recommended for beginners, due to the way they are supposed to be built following specific rules and orders according to the .rtf and .prm files.

One specific way I have tried is by using the VMD plugin called AutoPSF, but it always ends up with 1 unparameterized component, which I am not sure how to go about.

Can anyone provide me some ideas as to how generating a .psf file for a fullerene should be approached? Is it really so difficult (I have been stuck for at least 2 weeks now)? Can you recommend some good sources that can help me do this?

Let me know if I can provide you with any more details.

Attached Files
C240-F-1.txt (48.82 KB, 15 downloads)
SHA1: 91d29fb7bd63e11511795888ecefafba9ad9635d
Last edited by FlickerBeam; 06/29/21 02:12 PM.
Re: Starter - How to create a correct .psf file (carbon)
FlickerBeam #38295 06/29/21 03:35 PM
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rmv Online Content
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The CHARMM force field is designed for discrete small molecules, either as single residues, or polymers of small residues with a small number of well defined linkages. While fullerenes might be reasonable to attempt, large sheets like graphene or nanotubes with variable registration of the how the tube is sealed pose challenges for tools designed for residue based biological force fields. As it stands, you would first need to create a residue that defines the complete fullerene or nanotube, which can be used to create a PSF.

Since you've used Avogadro, one thing you might try is export the structure as a .mol2 file and then use the cgenff tool to create the residue and assign the atom parameter types and bond based parameters. As usual, no warranty expressed or implied.

There are some (older) discussions of nanotubes in the parameter forum.

The charmm-gui site has some facilities for building nanotubes.

Last edited by rmv; 06/29/21 08:32 PM. Reason: charmm-gui

Rick Venable
computational chemist


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